file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 13.00 17.00 18.00 17.82 19.00 21.00
## [1] 40
## [1] 13 14 15 16 17 17 17 17 17 17 17 17 17 17 17 18 18 18 18 18 18 18 18 18 18
## [26] 18 18 19 19 19 19 19 19 19 19 19 20 20 20 21
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"
##
## FALSE TRUE
## 1951 49
##
## FALSE TRUE <NA>
## 45 1906 49
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ADPRHL2 ADPRS
## 2: AES TLE5
## 3: C12orf45 NOPCHAP1
## 4: C3orf58 DIPK2A
## 5: C6orf99 LINC02901
## 6: CBWD2 ZNG1B
## 7: CXorf57 RADX
## 8: FAM102A EEIG1
## 9: FAM122C PABIR3
## 10: FAM153C FAM153CP
## 11: FAM160A2 FHIP1B
## 12: GRASP TAMALIN
## 13: H2AFX H2AX
## 14: HIST1H2AG H2AC11
## 15: HIST1H2BC H2BC5
## 16: HIST1H2BK H2BC12
## 17: HIST1H2BN H2BC15
## 18: HIST1H3A H3C1
## 19: HIST1H3H H3C10
## 20: HIST1H4C H4C3
## 21: HIST2H2BF H2BC18
## 22: LRMP IRAG2
## 23: MFSD14C MFSD14CP
## 24: MKL1 MRTFA
## 25: MPP6 MPHOSPH6
## 26: RNASEH1-AS1 RNASEH1-DT
## 27: SEPT6 SEPTIN6
## 28: SEPT9 SEPTIN9
## 29: TMEM161B-AS1 TMEM161B-DT
## 30: ARNTL BMAL1
## 31: C6orf106 ILRUN
## 32: C6orf203 MTRES1
## 33: FAM129A NIBAN1
## 34: FAM160B1 FHIP2A
## 35: FAM192A PSME3IP1
## 36: HEXDC HEXD
## 37: HIST1H1E H1-4
## 38: KIAA0100 BLTP2
## 39: KIAA1551 RESF1
## 40: LARS LARS1
## 41: MARS MARS1
## 42: PLA2G16 PLAAT3
## 43: SEPT2 SEPTIN6
## 44: SMIM37 MTLN
## 45: YARS YARS1
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: ABCD3 ABCD3 ABCD3
## 2: ABCG1 ABCG1 ABCG1
## 3: ABHD5 ABHD5 ABHD5
## 4: ABI1 ABI1 ABI1
## 5: ABLIM1 ABLIM1 ABLIM1
## t1
## 1 2
## 1998 1
## sym_in_data sym_limma gene_symbol
## 1: SEPT6 SEPTIN6 SEPTIN6
## 2: SEPT2 SEPTIN6 SEPTIN6
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"
## reactome go_bp immune
## 1692 7647 5219
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992
## [1] 2000 3
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.1)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "AC004854.2" "BX284668.6" "KCNQ1OT1" "ARHGAP10" "CARD11"
## [6] "CCL5" "CCR4" "FAM53B" "IRF9" "LTBP3"
## [11] "MYO1F" "NEAT1" "PPRC1" "SH3BP2" "VCAN"
## [16] "ZEB2" "ZNF267"
## [1] 2
## [1] "AC116407.2" "ADGRG1" "APOL1" "BISPR" "CCL4"
## [6] "CD300A" "GPR132" "GPR65" "GRK2" "LINC01871"
## [11] "MIAT" "MIR4435-2HG" "MYBL1" "S1PR5" "TSPAN32"
## [16] "USP30-AS1" "ZNF683"
## [1] 3
## [1] "AC008105.3" "AC025171.2" "BOLA2-SMG1P6" "C12orf29" "IGLV1-44"
## [6] "LINC01215" "LRMP" "MDS2" "PLCL1" "RETREG1"
## [11] "RNASEH1-AS1" "TRAV12-1" "TRAV12-2" "TRAV21" "TRAV25"
## [16] "TRAV38-2DV8" "TRAV8-6" "TRBV5-4" "TRBV6-5" "ZNF600"
## [21] "ZNF749"
## [1] 4
## [1] "AC004687.1" "GOLGA8B" "GZMK" "LST1" "NUP58"
## [6] "PARP8" "PLEKHM1" "RABL2B" "RGS1" "TECPR1"
## [11] "ZNF10" "ABHD3" "NKG7" "NRDC" "PPP2R3C"
## [16] "SPON2" "TGFBR3"
## [1] 5
## [1] "ABCG1" "CD28" "DSE" "ERCC5" "LRRC8D" "MAP3K8" "MZF1"
## [8] "PLK3" "EFR3A" "FAM129A" "GMFB" "GNPTAB" "ISG20" "MYO1G"
## [15] "PTGER2" "RNF19A" "SYTL1" "TGS1" "TRIB2"
## [1] 6
## [1] "AC145124.1" "AP002360.1" "DNASE1" "FAM122C" "FBXO8"
## [6] "GIMAP6" "JAML" "KCNK6" "LRRN3" "NUAK2"
## [11] "RPS26" "SLC25A38" "TRAV23DV6" "TRAV41" "XIST"
## [16] "ZNF140" "ZNF84"
## [1] 7
## [1] "GGT7" "ZNF490" "ASCL2" "BCL9L" "CCDC112" "CD58" "EHMT1"
## [8] "GALNS" "GBP1" "GBP3" "GBP5" "GZMH" "HIVEP3" "IFI35"
## [15] "KLF9" "RAB8B" "SCAF8" "TBX21"
## [1] 8
## [1] "CD40LG" "GIMAP1" "IGKV1-5" "IGKV3-20" "LAX1" "MBNL2"
## [7] "NBPF14" "NUDT4" "PCMTD2" "PDE7A" "PYROXD1" "SLC26A11"
## [13] "SPIDR" "TUBD1" "TUBE1" "ZNF677" "SUSD6"
## [1] 9
## [1] "C16orf74" "FAM153C" "GRASP" "LYRM7" "STARD10" "STX16"
## [7] "TOB2" "YPEL2" "ZNF831" "ZSCAN18" "ABHD2" "FAM160B1"
## [13] "FRY" "FRYL" "NBEAL2" "PEX26" "SUGP2"
## [1] 10
## [1] "AC023157.3" "AC025171.3" "AL121944.1" "AL135791.1" "AL359220.1"
## [6] "AL627171.1" "AL645728.1" "C6orf99" "LINC02273" "NDUFV2-AS1"
## [11] "NSMCE3" "PRR7" "AC016831.7" "AKNA" "AREG"
## [16] "ATAD2B" "CEMIP2" "TENT5C" "THUMPD3-AS1"
## [1] 11
## [1] "IER3" "C1orf21" "CMIP" "CROT" "DIP2A" "EIF2AK4"
## [7] "GABPB2" "KLHDC4" "NQO2" "PLA2G16" "PPP2R5B" "PREX1"
## [13] "PTGDR" "RBSN" "RNPEPL1" "SACS" "TNFRSF18" "ZNF236"
## [1] 12
## [1] "AC245297.3" "MUC20-OT1" "OTULINL" "ZFP14" "ADGRE5"
## [6] "CARD16" "GIMAP7" "GZMM" "HACD3" "KANSL1-AS1"
## [11] "KIAA0040" "LY6E" "MFSD14A" "NBDY" "NDUFC1"
## [16] "RAP1GAP2" "SLFN12L" "TM2D1" "TRANK1" "TUT4"
## [1] 13
## [1] "CRLF3" "GIMAP8" "HOXB2" "IGLV2-14" "MAST4" "ODF2L"
## [7] "SIMC1" "THAP6" "ZFX" "DENND4B" "FCRL6" "IFI44"
## [13] "IFI44L" "MX2" "OAS1" "OAS2" "PHF23" "PRSS23"
## [19] "RSAD2"
## [1] 14
## [1] "ADPRHL2" "ANKH" "MHENCR" "NEU1" "ZNF821" "ABCC1" "G2E3"
## [8] "HEXDC" "MLLT10" "MLLT6" "MYOM2" "PARP4" "TIPARP" "TSPAN14"
## [15] "TUBGCP6" "WDR43" "ZNF708"
## [1] 15
## [1] "AC007952.4" "AC119396.1" "AC245014.3" "AL138963.3" "ARHGAP15"
## [6] "ATP5MG" "CITED2" "FCMR" "FYB1" "LIMD2"
## [11] "MTRNR2L12" "NOP53" "RACK1" "SCML4" "SNHG8"
## [16] "TBC1D10C" "TC2N" "TNFRSF25" "WAPL"
## [1] 16
## [1] "KIF9" "TRBV7-3" "ABCC10" "AP3M2" "C4orf48" "COL6A3" "CRTC3"
## [8] "CTBS" "CYTIP" "GPRIN3" "LAIR2" "SBNO2" "SDR39U1" "SLC9A8"
## [15] "STK17B" "TAF4B" "TMEM156"
## [1] 17
## [1] "AC015982.1" "AC016405.3" "AC083880.1" "AC091271.1" "AC103591.3"
## [6] "AF213884.3" "AL357060.1" "AL451085.1" "ARF4-AS1" "HIPK1-AS1"
## [11] "ID3" "LINC01465" "MZF1-AS1" "NOCT" "NPIPB11"
## [16] "NPIPB4" "OSER1-DT" "SDR42E2" "THAP9-AS1" "TRBV6-6"
## [1] 18
## [1] "ENOSF1" "FAM227B" "NSUN6" "TBCCD1" "CFD" "CRYBG1"
## [7] "ECPAS" "ITK" "LPIN1" "LPIN2" "NNT-AS1" "ODF3B"
## [13] "RTKN2" "SAMD9L" "TOMM70" "TRBV6-1" "TTC16" "Z93930.2"
## [19] "ZBP1"
## [1] 19
## [1] "ANK3" "ATXN7L3B" "CCDC88B" "CISH" "ICE1" "IFNGR2"
## [7] "KHNYN" "NFKBIZ" "P4HTM" "PIEZO1" "PRDM1" "SESN3"
## [13] "SLC20A2" "TOB1" "TSHZ2" "UGCG" "ZNF101" "ZNF593"
## [1] 20
## [1] "KLF10" "SH3YL1" "ATP8B2" "CD69" "CITED4" "CRIP2" "DDIT4"
## [8] "HELB" "ICOS" "KCNAB2" "KIF21B" "NPDC1" "PKNOX1" "PREP"
## [15] "REXO2" "SLC35A2" "TBC1D14" "ZDHHC20"
## [1] 21
## [1] "AIF1" "CCDC66" "RASA2" "SENP7" "SIAH2" "TBPL1" "CHD6"
## [8] "ERICH1" "GNLY" "MT2A" "NCOA7" "NLRC5" "PCED1B" "RAPGEF1"
## [15] "STAT4" "STK10" "TNFRSF4" "XAF1"
## [1] 22
## [1] "ARL6IP1" "CCDC141" "CENPK" "CXorf57" "PHYH" "SLC38A2" "TSC22D2"
## [8] "WARS2" "ADAM19" "CREBZF" "GNPAT" "NARF" "NFE2L1" "SETD5"
## [15] "SH3BP5" "SLA" "SMAP1" "SNX1" "XBP1"
## [1] 23
## [1] "AC009061.2" "AC020911.2" "AC025164.1" "AC084033.3" "AC087239.1"
## [6] "AL118516.1" "ATP2B1-AS1" "CERNA1" "CSKMT" "IL23A"
## [11] "ILF3-DT" "LYRM9" "MATR3-1" "Z93241.1" "AC020915.3"
## [16] "SNHG9"
## [1] 24
## [1] "SNHG7" "AC022916.1" "CARD8-AS1" "CTSW" "CX3CR1"
## [6] "FGFBP2" "IL21R" "KIF21A" "MCTP2" "NAA38"
## [11] "PAXX" "PLEK" "RASAL3" "TRAV29DV5" "TRBV12-3"
## [1] 25
## [1] "CARHSP1" "CCDC18" "CEP120" "CEP95" "CHIC2" "COG5" "LCLAT1"
## [8] "MAP3K2" "NSMAF" "PECAM1" "POC5" "SBF2" "SNX18" "FNDC3B"
## [15] "GCA" "LAG3" "SBF1"
## [1] 26
## [1] "JPX" "APH1B" "ARHGEF3" "DTX3L" "ETNK1" "IRAK4" "NT5C"
## [8] "PARP14" "PARP9" "PDE4B" "PLAC8" "PRDM2" "RCBTB2" "RNF145"
## [15] "RNMT" "SEC14L1" "SP140L" "ZNF292"
## [1] 27
## [1] "ANKRD44" "C6orf62" "INPP4B" "MAML2" "PECR" "PHC1" "PLK2"
## [8] "TPP2" "WASHC4" "ADTRP" "DOCK2" "PCGF5" "PYCARD" "SOCS2"
## [15] "TAOK3" "VPS36" "ZNF276"
## [1] 28
## [1] "LRRC8C-DT" "FAAH2" "GIMAP4" "HRH2" "IFITM2" "LRRC58"
## [7] "MT1X" "NORAD" "PARP11" "PCSK1N" "PUM3" "S100A12"
## [13] "SLC25A37" "SLF2" "SMIM37" "SPATA13" "TCAF2" "UBALD2"
## [19] "UTP25"
## [1] 29
## [1] "ATG9B" "CFAP36" "DIP2B" "FBXO3" "HELQ" "IL6R"
## [7] "KLHL6" "LTB" "OSER1" "PLCD1" "RCAN3" "SLC22A17"
## [13] "STK19" "TBCC" "TBCK" "TGIF1" "TTC39C" "C12orf4"
## [1] 30
## [1] "AL133415.1" "C1GALT1" "DPYD" "KLF7" "LEPROT"
## [6] "LINC01550" "POLD4" "RAB33B" "RAB37" "SLC7A6"
## [11] "SPART" "TMEM204" "TRABD2A" "TRAV8-3" "XRRA1"
## [16] "ZMAT1" "ZNF506" "ANKAR" "APOL6" "GAB3"
## [1] 31
## [1] "BTN3A1" "C17orf49" "CTSF" "ERAP2" "EVI2B"
## [6] "HIVEP2" "IPCEF1" "METAP1" "MTO1" "ORC4"
## [11] "PITPNA-AS1" "TMEM154" "TMEM245" "WHAMM" "YY1AP1"
## [16] "BTN3A2" "KLRG1" "TMEM175"
## [1] 32
## [1] "AC027644.3" "AC087623.3" "AC093323.1" "AC097376.2" "AK5"
## [6] "AL139246.5" "ARRDC2" "CHRM3-AS2" "COX10" "ERVK3-1"
## [11] "GPCPD1" "LETM2" "LINC00649" "ST7L" "TRAV13-2"
## [16] "TRAV14DV4" "TRAV9-2" "TRBV28" "FRMD4B"
## [1] 33
## [1] "COA1" "MBD6" "NR4A3" "AGAP2" "AZI2" "B3GALT4" "KIF3B"
## [8] "N4BP1" "PDE12" "PIP4K2B" "RECK" "SIGIRR" "SLC23A2" "TBC1D15"
## [15] "TMX3" "TRMT10C" "UBA7"
## [1] 34
## [1] "ATF4" "BTG2" "FBXL3" "HEATR5B" "LDLRAP1" "MTERF4" "OXLD1"
## [8] "BATF" "DDX41" "IFNAR1" "LPCAT3" "MAF" "PVT1" "SYNRG"
## [1] 35
## [1] "ACADSB" "ARID4A" "ATAD1" "DAPP1" "DBP" "FAM118A"
## [7] "HDHD2" "ING2" "INTS6" "MXD1" "NABP1" "PPP1R15B"
## [13] "SGSM3" "SLC25A33" "TIA1" "UBL3" "UCP2" "CAST"
## [19] "GZMB"
## [1] 36
## [1] "ADA2" "COQ10A" "JCHAIN" "LINC00623" "LINC02265"
## [6] "MFSD14C" "MLXIP" "MMP28" "NAA16" "NPIPB5"
## [11] "TMEM161B-AS1" "TMEM71" "TRAV8-2" "ZNF91" "AC118549.1"
## [16] "IGLV3-25" "TMEM138" "TTC38"
## [1] 37
## [1] "ABHD5" "AC013264.1" "CAMK4" "GCH1" "IFRD1"
## [6] "KIAA1328" "KLRB1" "MID1IP1" "NRIP1" "OTUD5"
## [11] "PHLDA1" "POU2F2" "RGCC" "SNRK" "TLE4"
## [16] "TOX" "TSPYL4" "ZFAS1"
## [1] 38
## [1] "ATG13" "C3orf58" "CD38" "FCGR3A" "FCN1" "HIST1H3H"
## [7] "IER5" "LIPT1" "RIC1" "TBC1D7" "TMC8" "TTC31"
## [13] "ZBTB25" "ZC3H12A" "ZC3H12D" "APOBEC3G" "GZMA" "MATK"
## [1] 39
## [1] "C20orf204" "CARMIL2" "DDX3Y" "EIF1AY" "KDM5D" "LY96"
## [7] "OSM" "RNF157" "RPS4Y1" "SOCS3" "TTTY15" "UTY"
## [13] "ZFYVE28"
## [1] 40
## [1] "ANXA2R" "ARL4A" "COQ10B" "COQ7" "COQ8A" "EFCAB2" "EGR1"
## [8] "ODC1" "SNHG12" "TAGAP" "TCP11L2" "TCTA" "WSB1" "APBB1IP"
## [15] "ARL4C" "BUD23" "CCDC43" "UBE3B"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_2"
## [1] "AC116407.2" "ADGRG1" "APOL1" "BISPR" "CCL4"
## [6] "CD300A" "GPR132" "GPR65" "GRK2" "LINC01871"
## [11] "MIAT" "MIR4435-2HG" "MYBL1" "S1PR5" "TSPAN32"
## [16] "USP30-AS1" "ZNF683"
## $reactome
## category over_represented_pvalue
## 158 class a 1 rhodopsin like receptors 1.215063e-06
## 413 gpcr ligand binding 7.213076e-06
## 359 g alpha q signalling events 1.337138e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 158 1.0000000 4 16 0.001459290
## 413 0.9999999 4 24 0.004331452
## 359 0.9999980 3 18 0.053530101
##
## [1] "set_7"
## [1] "GGT7" "ZNF490" "ASCL2" "BCL9L" "CCDC112" "CD58" "EHMT1"
## [8] "GALNS" "GBP1" "GBP3" "GBP5" "GZMH" "HIVEP3" "IFI35"
## [15] "KLF9" "RAB8B" "SCAF8" "TBX21"
## $go_bp
## category
## 693 disruption of anatomical structure in another organism
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 693 8.708209e-06 0.9999999 4 17
## FDR
## 693 0.04165136
##
## [1] "set_13"
## [1] "CRLF3" "GIMAP8" "HOXB2" "IGLV2-14" "MAST4" "ODF2L"
## [7] "SIMC1" "THAP6" "ZFX" "DENND4B" "FCRL6" "IFI44"
## [13] "IFI44L" "MX2" "OAS1" "OAS2" "PHF23" "PRSS23"
## [19] "RSAD2"
## $reactome
## category over_represented_pvalue
## 476 interferon alpha beta signaling 4.578903e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 476 0.999999 4 38 0.05499263
##
## $immune
## category
## 4937 hoek neutrophil 2011 2012 tiv adult 7dy dn
## 4935 hoek neutrophil 2011 2012 tiv adult 1dy up
## 5062 querec pbmc yf 17d vaccine age 18 45yo 3dy up
## 5063 querec pbmc yf 17d vaccine age 18 45yo 7dy up
## 5102 zak pbmc mrkad5 hiv 1 gag pol nef age 20 50yo 3dy up
## 2127 gse24081 controller vs progressor hiv specific cd8 tcell dn
## 4047 gse42021 tconv pln vs cd24hi tconv thymus dn
## 13 erwin cohen blood vaccine tc 83 age 23 48yo vaccinated vs control 7dy up
## 54 gaucher pbmc yf vax stamaril unknown age 3dy up
## 1289 gse17974 il4 and anti il12 vs untreated 24h act cd4 tcell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4937 3.906394e-08 1.0000000 5 12
## 4935 3.942643e-08 1.0000000 5 12
## 5062 8.714928e-08 1.0000000 6 27
## 5063 8.714928e-08 1.0000000 6 27
## 5102 8.835708e-08 1.0000000 7 45
## 2127 1.594941e-07 1.0000000 7 48
## 4047 5.380862e-07 1.0000000 6 35
## 13 8.030557e-07 1.0000000 6 38
## 54 1.921617e-06 0.9999999 7 69
## 1289 2.555537e-06 0.9999999 6 45
## FDR
## 4937 9.023025e-05
## 4935 9.023025e-05
## 5062 9.023025e-05
## 5063 9.023025e-05
## 5102 9.023025e-05
## 2127 1.357294e-04
## 4047 3.924954e-04
## 13 5.125503e-04
## 54 1.090197e-03
## 1289 1.255580e-03
##
## [1] "set_18"
## [1] "ENOSF1" "FAM227B" "NSUN6" "TBCCD1" "CFD" "CRYBG1"
## [7] "ECPAS" "ITK" "LPIN1" "LPIN2" "NNT-AS1" "ODF3B"
## [13] "RTKN2" "SAMD9L" "TOMM70" "TRBV6-1" "TTC16" "Z93930.2"
## [19] "ZBP1"
## $reactome
## category over_represented_pvalue
## 1170 triglyceride biosynthesis 2.644597e-05
## 1073 synthesis of pe 8.478266e-05
## 230 depolymerization of the nuclear lamina 2.710994e-04
## 1172 triglyceride metabolism 2.980980e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 1170 1.0000000 2 2 0.03176161
## 1073 0.9999999 2 3 0.05091199
## 230 0.9999989 2 5 0.08950393
## 1172 0.9999987 2 5 0.08950393
##
## [1] "set_25"
## [1] "CARHSP1" "CCDC18" "CEP120" "CEP95" "CHIC2" "COG5" "LCLAT1"
## [8] "MAP3K2" "NSMAF" "PECAM1" "POC5" "SBF2" "SNX18" "FNDC3B"
## [15] "GCA" "LAG3" "SBF1"
## $immune
## category
## 5031 nakaya pbmc fluarix fluvirin age 18 50yo correlated with hai 28dy response at 7dy
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 5031 1.650058e-05 0.9999997 4 19
## FDR
## 5031 0.08425197
##
## [1] "set_31"
## [1] "BTN3A1" "C17orf49" "CTSF" "ERAP2" "EVI2B"
## [6] "HIVEP2" "IPCEF1" "METAP1" "MTO1" "ORC4"
## [11] "PITPNA-AS1" "TMEM154" "TMEM245" "WHAMM" "YY1AP1"
## [16] "BTN3A2" "KLRG1" "TMEM175"
## $reactome
## category over_represented_pvalue
## 110 butyrophilin btn family interactions 4.716898e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 110 1 2 2 0.05664994
##
## [1] "set_39"
## [1] "C20orf204" "CARMIL2" "DDX3Y" "EIF1AY" "KDM5D" "LY96"
## [7] "OSM" "RNF157" "RPS4Y1" "SOCS3" "TTTY15" "UTY"
## [13] "ZFYVE28"
## $immune
## category
## 827 gse16450 immature vs mature neuron cell line 6h ifna stim dn
## 4353 gse5099 classical m1 vs alternative m2 macrophage dn
## 3753 gse39820 ctrl vs il1b il6 cd4 tcell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 827 3.999097e-06 0.9999999 4 20
## 4353 5.322847e-06 0.9999999 4 21
## 3753 5.694788e-06 0.9999998 5 48
## FDR
## 827 0.009692529
## 4353 0.009692529
## 3753 0.009692529
##
## [1] "set_40"
## [1] "ANXA2R" "ARL4A" "COQ10B" "COQ7" "COQ8A" "EFCAB2" "EGR1"
## [8] "ODC1" "SNHG12" "TAGAP" "TCP11L2" "TCTA" "WSB1" "APBB1IP"
## [15] "ARL4C" "BUD23" "CCDC43" "UBE3B"
## $go_bp
## category over_represented_pvalue
## 1257 ketone biosynthetic process 3.484787e-07
## 4687 ubiquinone metabolic process 5.953627e-06
## 3236 quinone metabolic process 2.038389e-05
## 395 cellular ketone metabolic process 7.898762e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1257 1.0000000 4 8 0.001666774
## 4687 1.0000000 3 5 0.014238099
## 3236 0.9999999 3 7 0.032498709
## 395 0.9999975 4 29 0.094449448
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958285 478.5 16391124 875.4 NA 16391124 875.4
## Vcells 19171499 146.3 57912627 441.9 65536 77218972 589.2
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1